Rerun_Fn: Explore counter-factual scenario

Description Usage Arguments Value

View source: R/Rerun_Fn.R

Description

Rerun_Fn re-builds a model while fixing a subset of parameters at zero

Usage

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Rerun_Fn(parhat0, turnoff_pars, loc_x,
  cov_to_turnoff = 1:dim(parhat[["gamma2_ctp"]])[3], calculate_COG = TRUE,
  figname = NULL, Map = "generate", MapDetails_List = NULL,
  year_set = 1:ncol(parhat0[["beta1_ct"]]),
  c_set = 1:nrow(parhat0[["beta1_ct"]]), ...)

Arguments

parhat0

parameter values to use by default (presumably maximum-likelihood estimates)

turnoff_pars

character-vector of parameters to turn off

loc_x

location for each knot used to calculate center-of-gravity for counter-factual runs with colnames c('E_km','N_km','Lon','Lat')

cov_to_turnoff

which covariates to turn off, as indicated by their order in TmbData$X_xtp (which only matters if "gamma1_ctp" or "gamma2_ctp" is in turnoff_pars)

calculate_COG

Boolean whether to calculate COG for each run

figname

name for figure to plot density in counter-factual scenario

Map

OPTIONAL, a tagged list of parameters to either mirror or turn off

MapDetails_List

output from SpatialDeltaGLMM::MapDetails_Fn

year_set

set of parameters to include

c_set

set of categories to include

...

additional arguments passed to VAST::Build_TMB_Fn

Value

Tagged list

Report

Report output for counter-factual run

NewBuild_List

Output from VAST::Build_TMB_Fn using counter-factual parameters


James-Thorson/VAST documentation built on Dec. 17, 2017, 11:35 p.m.